VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Jun 12 2013 - 23:19:30 CDT

Hi,
  Something went wrong with your parameter file as NAMD can't find
the params for some of those atoms. If you still need help with this,
you're going to have to tell exactly what steps you followed, as there
may be issues at any point along the path to building and merging these
structures. Also, it is good form to keep vmd-l in your CC list since
that's where the question originated, so that others can chime in when
I get bogged down with too many emails, as happened this time.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Jun 03, 2013 at 05:57:24PM +0000, Anurag Sharma wrote:
> Hi John,
>
> I have installed 1.9.2 alpha version and now am able to merge oligemer chain and carbon nanotube. I am using CHARMm parameter file to run merge structures in NAMD. I encountered another problem while running these simualtions in NAMD.
> "FATAL ERROR: UNABLE TO FIND IMPROPER PARAMETERS FOR CA CA CA CA (ATOMS 822 1 2 188)"
> CA = carbon atoms in carbon nanotube
>
> Do I need to generate topology file for carbon nanotube to correct this error?
>
> Thanks
>
> Anurag Sharma
>
> ________________________________________
> From: Anurag Sharma
> Sent: Wednesday, May 22, 2013 10:56 AM
> To: John Stone
> Subject: RE: vmd-l: error in merging two structures
>
> Hi John,
>
> Thanks for the reply. I will register and install the newer version. I'll let you know the outcome.
>
> Anurag
>
> ________________________________________
> From: John Stone [johns_at_ks.uiuc.edu]
> Sent: Wednesday, May 22, 2013 10:24 AM
> To: Anurag Sharma
> Cc: vmd-l_at_ks.uiuc.edu
> Subject: Re: vmd-l: error in merging two structures
>
> Hi,
> I would suggest that you try one of the newer versions of VMD
> which has updates to several of the tools you used below. It may
> or may not solve the problem, but if the problem persists, it would
> be much easier to track down in the current version of the code.
> You can get the test versions of VMD 1.9.2 by following the instructions
> posted here:
> http://www.ks.uiuc.edu/Research/vmd/alpha/
>
> Let us know if using the new VMD test version has any impact on
> the problem you have been having.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Mon, May 20, 2013 at 05:38:18PM +0000, Anurag Sharma wrote:
> > Dear all,
> >
> > I created a (10,10) carbon nanotube with Nanotube Builder and created psf
> > and pdb by typing
> >
> > "animate write psf cnt.psf"
> > "animate write pdb cnt.pdb"
> >
> > psf and pdb files were successfully created (no problem regarding
> > bonds,angles etc.) and then I wanted to merge it with a oligomer chain.
> > So I used merge structure plugin in VMD.
> >
> > Then I got an error message saying
> >
> > MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
> >
> > MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
> > while executing
> > "readpsf $m1psf"
> > invoked from within
> > "psfcontext eval $psfcon {
> > # this is a hack, just to get the topology file
> > package require readcharmmtop
> > set topologyfile [format "%s/top_a..."
> > (procedure "mergeMolecules" line 6)
> > invoked from within
> > "mergeMolecules [list "$guiState(mergef1src).psf"
> > "$guiState(mergef1src).pdb" ] [list "$guiState(mergef2src).psf"
> > "$guiState(mergef2src).pdb" ] $gu..."
> > (procedure "::MergeStructs::guiMergeConflictsResolved" line 6)
> > invoked from within
> > "::MergeStructs::guiMergeConflictsResolved"
> > ("after" script)
> >
> >
> >
> > Interstingly I have also tried to merge (9,9) and (8,8) carbon nanotubes
> > with same oligmer chains and I found no problem there. I follow same
> > procedures to generate carbon nanotubes and merging them with chains in
> > all cases.
> >
> > I am using VMD 1.9.1 and nanotube 1.2 version.
> >
> >
> >
> > Thanks
> >
> > Anurag
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/ 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/